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The worst job in the world, western spymasters used to joke, was being number three in al-Qaeda.

At its peak, the US drone programme– with Hellfire missiles picking off al-Qaeda leaders seemingly at will in the remote mountains of Yemen and the tribal borderlands of Pakistan – meant becoming number three was as good as being dead.

But al-Qaeda has proved to have a Hydra-like quality. Far from withering, it has proliferated. The group and its affiliates have never controlled more land, had as many recruits in their ranks or been as well financially resourced as now.

In recent months, al-Qaeda franchises have scored successes or near-victories in an arc stretching from the Sahel in east Africa through to the Levant via the Horn of Africa, Yemen and Iraq.

In 2012, al-Qaeda forces came within hours of seizing control of Bamako, the capital of Mali. In 2013, its militants radicalised the conflict in Syria. This year has begun with fighters storming the city of Fallujah in Iraq, just 70km from Baghdad. They still control it.

Last Wednesday, the US House Intelligence committee opened an inquiry to investigate the resurgence of the group. Mike Rogers, the Republican congressman who chairs the committee, called the demise of al-Qaeda a “false narrative” and warned against complacency in Washington. He cautioned: “The defeat of an ideology requires more than just drone strikes.”

Affiliates around the world

Afghanistan and Pakistan

Syria and Iraq

Yemen

Horn of Africa

The Sahel and Maghreb

Three fundamental questions are of concern to the west in its handling of the group’s rebound. How resilient is the resurgence, how centralised is its structure and how much of a threat does it still pose internationally?

The hope among its opponents is that al-Qaeda’s renaissance belies a still dangerous but fatally weakened foe. Many see the group as a disparate set of franchises that have fed off disenchantment caused by the Arab Spring, but which ultimately are either locally focused and pragmatic. Or they believe it will burn itself out through its own brutality, alienating local Muslim populations by persecuting them as much as waging jihad against the west and its regional allies.

They point to the situation in Syria, where jihadis fighting for the Islamic State of Iraq and al-Sham are committing atrocities against civilians, turning other Islamist groups against them.

But Isis’s brutality – and the “seeds of its own destruction” narrative of al-Qaeda that is perpetuated by such actions in the west – is far from the complete picture.

Al-Qaeda is certainly disparate and no longer controlled to the same degree by a central authority. But it has proved very adaptable, and very aware of the mistakes it made in the past.

Afghanistan and Pakistan

In Afghanistan, the rout of al-Qaeda has been extensive. Intelligence analysts put the number of al-Qaeda operatives functioning in the country as low as 200, although many fear a rebound if aid to the fragile Afghan government dries up.

For now, al-Qaeda’s core presence in the area – and the world – remains in Pakistan, where Ayman al-Zawahiri, the successor to Osama bin Laden, is based.

Its links in Pakistan run deep. It is telling that it took the US a decade to find the whereabouts of bin Laden, who turned out to be living in a compound in urban Abbottabad. While al-Qaeda is known to have a significant presence in the Federally Administered Tribal Areas of the country, many analysts believe its core leadership operates comfortably – or could even be based in – its most populated, metropolitan areas.

The US drone campaign explains why. “You can’t just go and bomb an urban area,” says Shashank Joshi, research fellow at the Royal United Services Institute, a UK think-tank. “Al-Qaeda has adapted to our counterterrorism measures and it has become more resilient. [While] its leadership has been shattered at various points, it is clearly not any longer an organisation dependent on a small coterie of individuals for its survival.”

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Syria and Iraq

It is now difficult to imagine that before the 2003 US invasion of Iraq, al-Qaeda and affiliated groups had almost no presence in the Levant. The ill-fated US occupation created both a lawless environment for radical jihadi governments to take root and fomented an ideologically potent cause for them to pursue.

Al-Qaeda’s early success in Iraq under Jordanian Abu Musab al-Zarqawi was unwound from 2006, thanks to the US-funded sahwa (awakening) of local Sunni tribes in Iraq’s Anbar province, who revolted against al-Qaeda’s excesses. It has since been resurgent. In Syria, the relentless and brutal assault on mostly peaceful Sunni protesters by Bashar al-Assad, the country’s Alawite president, has provided al-Qaeda with an expansive presence in the region. In Iraq, political mismanagement on the part of President Nouri al-Maliki and the spillover from Syria have contributed to the group’s renewed presence in Anbar province.

Both Jahbat Al-Nusra, led by Abu Mohammed al-Joulani, and the Islamic State of Iraq and al-Sham, led by Abu Bakr al-Baghdadi, claim affiliation to al-Qaeda in the region.

But in Syria, it is Al-Nusra – Syrian- led and more tolerant – that has the support of Mr Zawahiri, and not the more brutal Iraqi-dominated Isis, which has already alienated swaths of the indigenous Syrian population with its ruthlessness.

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Yemen

The remote mountains of southern Yemen gave birth to al-Qaeda and to this day remain one of the group’s most cohesive strongholds in the world. The group has found solace among the mountains and fiercely independent tribes of the south, tapping into the deep pool of resentment born of grinding poverty, anti-northern sentiment and, more recently, US drone strikes that have all too often hit innocent targets.

The Yemeni and Saudi branches of the group merged in 2009 to form al-Qaeda in the Arabian Peninsula, led by Nasir al-Wuhaishi, Osama bin Laden’s former secretary and one of Mr Zawahiri’s closest allies. AQAP is considered by western intelligence agencies the most dangerous branch of al-Qaeda, and it has proved resilient: a government campaign in 2012 to expel the group from Abyan and Sabwah provinces is still continuing.

AQAP has more recently adapted its method of exporting jihad by using other militant groups around the world as proxies.

“This may be the kind of relationship that we increasingly see between AQAP and other groups with the promotion of Mr Wuhaishi – loose operational guidance with seed funding and, where possible, the provision of fighters to participate in high-profile plots, especially in the fluid security environments of north Africa,” says John Nugent, terrorism analyst at Control Risks, a security consultancy.

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Horn of Africa

In the Horn, al-Qaeda’s current largest affiliate is al-Shabaab (the Boys), the former youth movement of the Islamic Courts Union (ICU), the radical Islamist group that once controlled most of Somalia.

While it has been forced to cede huge swaths of territory in the past 18 months, it remains a well-resourced organisation, and embedded throughout Somalia.

Yemen: Married into the system

The experience of al-Qaeda in Yemen highlights the group’s approach under Ayman al-Zawahiri’s leadership.

“I call on the noble and defiant tribes of the Yemen: Don’t be less than your brothers in the defiant Pashtun and Baluch tribes,” he said in 2009, identifying the region as a future haven for al-Qaeda, akin to the Federally Administered Tribal Area of Pakistan, the then remaining stronghold of the group.

Al-Qaeda has sought to entrench itself deeply with the local, rural tribal population. Its members have married into tribal groups. It has courted tribal leaders with money and aid. And it has ensured, under the regional leadership of Yemeni Nasir al-Wuhaishi, head of al-Qaeda in the Arabian Peninsula, that its recruits are mostly indigenous.

These are lessons learned directly from the Iraqi sahwa – the “awakening” of Sunni tribes, funded by the US in Iraq’s western provinces, who rose up against al-Qaeda’s brutal sharia rule and its divisive takfiri policies, meted out against fellow Muslims for doctrinal transgressions.

Avoiding the same mistake has made AQAP far more resilient. In Yemen drone strikes are increasingly a double-edged sword: every time a child or woman is killed as collateral damage, more jihadis are recruited to the AQAP cause.

The UN estimated it earned $50m a year when it controlled the port of Kismayo. It has also exploited the illegal ivory trade, killing hundreds of elephants in the region, according to environmental campaigners.

As al-Shabaab has been pushed back, it has sought to export violence to the home soil of those fighting it, such as Kenya. The group orchestrated the deadly Westgate shopping mall attack in Nairobi last September, in which more than 60 people died.

The ICU itself had strong ties with al-Qaeda core, with many of its founding leaders trained in Afghanistan, but al-Shabaab has often chosen to follow its own path.

In 2010 Mr Zawahiri sought to replace al-Shabaab’s leader, Ahmed Godane, but his ruling was ignored. Mr Godane swore allegiance to Mr Zawahiri again in 2012.

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The Sahel and Maghreb

More than a year after staging a spectacular attack on a remote Algerian oil and gas facility, and 18 months after nearly seizing control of Mali, al-Qaeda of the Islamic Maghreb appears on the defensive. French troops have pushed back AQIM, led by Abu Musab Abdel Wadoud, a veteran of Algeria’s 1990s civil war. Algeria’s security forces have cornered extremist groups.

But from Mauritania to Libya, the longstanding ethnic and political grievances still fester. The abuses of the civil war that fed Algerian Islamist anger have never been resolved. The official neglect that led ethnic Tuaregs to seek an autonomous Saharan homeland has worsened.

“No one should underestimate the narrow margin that existed between AQ and their goal of seeking to take over the organs of a whole state and create a safe haven,” says Stephen O’Brien, the UK prime minister’s special envoy to the Sahel, referring to AQIM’s near takeover of Bamako, Mali’s capital, in 2012.

“What is clear is that the franchise’s approach has become much more about winning over the hearts and minds of populations by the provision of basic services.”

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Different approach

Last month al-Qaeda broke new ground: it apologised. “We acknowledge our mistake and guilt,” Qassim al-Rimi, a commander of AQAP in Yemen, said in a video, referring to an attack on December 5 on the Yemeni Defence Ministry that killed 52 people – many in the attached hospital next door.

Behind the statement was recognition of the need to keep local populations onside, and the difficulties of doing so for such a violent, strict Islamist organisation.

The tension recurs frequently but al-Qaeda has shown that it has the will to resolve it.

If al-Qaeda’s threat to the west is perceived to have diminished, it is perhaps precisely because the group has learnt from the sahwa in Iraq and has been at pains to refocus on its core project: the establishment of al-Qaeda controlled “emirates” and, eventually, a larger caliphate. To do so, the group clearly recognises that it needs genuine and lasting popular support. It is why Mr Zawahiri supports Al-Nusra in Iraq and fell out with Mr Godane in Somalia.

After French troops pushed AQIM out of Timbuktu in Mali last year, journalists stumbled across a rare document: letters from AQIM’s leader, Abu Musab Abdel Wadoud, to his commanders.

“The current baby is in its first days, crawling on its knees, and has not yet stood on its two legs,” Wadoud wrote. “If we really want it to stand on its own two feet in this world full of enemies waiting to pounce, we must ease its burden, take it by the hand, help it and support it . . . until it stands.”